Finalize API and fix compatibility with BIDS

index.js

@@ -1,7 +1,3 @@
-import bids from './src/bids'
+export * from './src/bids'
 
-export { bids }
-
-export default {
-  bids,
-}
+export { IssueError } from './src/issues/issues'

src/bids/index.js

@@ -2,25 +2,13 @@ import { buildBidsSchemas } from './schema'
 import { BidsJsonFile, BidsSidecar } from './types/json'
 import { BidsTsvFile } from './types/tsv'
 import { BidsHedIssue } from './types/issues'
-import BidsHedSidecarValidator from './validator/sidecarValidator'
-import BidsHedTsvValidator from './validator/tsvValidator'
 
-export {
-  BidsTsvFile,
-  BidsJsonFile,
-  BidsSidecar,
-  BidsHedIssue,
-  BidsHedSidecarValidator,
-  BidsHedTsvValidator,
-  buildBidsSchemas,
-}
+export { BidsTsvFile, BidsJsonFile, BidsSidecar, BidsHedIssue, buildBidsSchemas }
 
 export default {
   BidsTsvFile,
   BidsJsonFile,
   BidsSidecar,
   BidsHedIssue,
-  BidsHedSidecarValidator,
-  BidsHedTsvValidator,
   buildBidsSchemas,
 }

src/bids/schema.js

@@ -11,12 +11,11 @@ const alphabeticRegExp = new RegExp('^[a-zA-Z]+$')
  * Build a HED schema collection based on the defined BIDS schemas.
  *
  * @param {BidsJsonFile} datasetDescription The description of the BIDS dataset being validated.
- * @param {SchemasSpec} schemaDefinition The version spec override for the schema to be loaded.
  * @returns {Promise} A Promise with the schema collection, or null if the specification is missing.
  * @throws {IssueError} If the schema specification is invalid.
  */
-export async function buildBidsSchemas(datasetDescription, schemaDefinition) {
-  const schemasSpec = buildSchemasSpec(datasetDescription, schemaDefinition)
+export async function buildBidsSchemas(datasetDescription) {
+  const schemasSpec = buildSchemasSpec(datasetDescription)
   if (schemasSpec === null) {
     return null
   }
@@ -27,28 +26,17 @@ export async function buildBidsSchemas(datasetDescription, schemaDefinition) {
  * Build a HED schema specification based on the defined BIDS schemas.
  *
  * @param {BidsJsonFile} datasetDescription The description of the BIDS dataset being validated.
- * @param {SchemasSpec} schemaDefinition The version spec override for the schema to be loaded.
  * @returns {SchemasSpec|null} The schema specification to be used to build the schemas, or null if the specification is missing.
  * @throws {IssueError} If the schema specification is invalid.
  */
-export function buildSchemasSpec(datasetDescription, schemaDefinition) {
-  if (schemaDefinition) {
-    return validateSchemasSpec(schemaDefinition)
-  } else if (datasetDescription.jsonData?.HEDVersion) {
+export function buildSchemasSpec(datasetDescription) {
+  if (datasetDescription.jsonData?.HEDVersion) {
     return parseSchemasSpec(datasetDescription.jsonData.HEDVersion)
   } else {
     return null
   }
 }
 
-function validateSchemasSpec(schemasSpec) {
-  if (schemasSpec instanceof SchemasSpec) {
-    return schemasSpec
-  } else {
-    IssueError.generateAndThrow('invalidSchemaSpecification', { spec: JSON.stringify(schemasSpec) })
-  }
-}
-
 export function parseSchemasSpec(hedVersion) {
   const schemasSpec = new SchemasSpec()
   const processVersion = castArray(hedVersion)

src/bids/types/file.js

@@ -59,7 +59,7 @@ export class BidsFile {
    * Validate this validator's tsv file.
    *
    * @param {Schemas} schemas - The HED schemas used to validate this file.
-   * @returns {BidsHedIssue[], BidsHedIssue[]} - Any issues found during validation of this TSV file.
+   * @returns {BidsHedIssue[]} - Any issues found during validation of this TSV file.
    */
   validate(schemas) {
     if (!this.hasHedData) {

src/bids/types/issues.js

@@ -1,26 +1,48 @@
+import groupBy from 'lodash/groupBy'
+
 import { generateIssue, IssueError } from '../../issues/issues'
 
 export class BidsHedIssue {
+  /**
+   * The file associated with this issue.
+   * @type {Object}
+   */
+  file
+  /**
+   * The HED Issue object corresponding to this object.
+   * @type {Issue}
+   */
+  hedIssue
   /**
    * The BIDS issue code.
    * @type {string}
    */
-  bidsCode
+  code
   /**
-   * The file associated with this issue.
-   * @type {Object}
+   * The HED spec code for this issue.
+   * @type {string}
    */
-  file
+  subCode
   /**
-   * The evidence for this issue.
+   * The severity of this issue.
    * @type {string}
    */
-  message
+  severity
   /**
-   * The HED Issue object corresponding to this object.
-   * @type {Issue}
+   * The issue message for this issue.
+   * @type {string}
    */
-  hedIssue
+  issueMessage
+  /**
+   * The line at which the issue was found.
+   * @type {number}
+   */
+  line
+  /**
+   * The location of the file at which the issue was found.
+   * @type {string}
+   */
+  location
 
   /**
    * Constructor.
@@ -30,60 +52,29 @@ export class BidsHedIssue {
    */
   constructor(hedIssue, file) {
     this.hedIssue = hedIssue
-    this.bidsCode = BidsHedIssue._determineBidsIssueCode(hedIssue)
-    this.message = hedIssue.message
     this.file = file
-  }
-
-  /**
-   * The HED spec code for this issue.
-   *
-   * @returns {string}
-   */
-  get hedCode() {
-    return this.hedIssue.hedCode
-  }
 
-  /**
-   * Whether this issue is an error.
-   *
-   * @returns {boolean}
-   */
-  get isError() {
-    return this.hedIssue.level === 'error'
+    // BIDS fields
+    if (hedIssue.level === 'warning') {
+      this.code = 'HED_WARNING'
+    } else {
+      this.code = 'HED_ERROR'
+    }
+    this.subCode = hedIssue.hedCode
+    this.severity = hedIssue.level
+    this.issueMessage = hedIssue.message
+    this.line = hedIssue.parameters?.tsvLine
+    this.location = file?.path
   }
 
   /**
-   * Determine if any of the passed issues are errors.
+   * Split a list of issues into errors and warnings.
    *
    * @param {BidsHedIssue[]} issues A list of issues.
-   * @returns {boolean} Whether any of the passed issues are errors (rather than warnings).
+   * @returns {Object<string, BidsHedIssue[]>} The list of issues divided into errors and warnings.
    */
-  static anyAreErrors(issues) {
-    return issues.some((issue) => issue.isError)
-  }
-
   static splitErrors(issues) {
-    const errors = issues.filter((item) => item.isError)
-    const warnings = issues.filter((item) => !item.isError)
-    return [errors, warnings]
-  }
-
-  /**
-   * Determine the BIDS issue code for this issue.
-   *
-   * @param {Issue} hedIssue The HED issue object to be wrapped.
-   * @returns {string} The BIDS issue code for this issue.
-   * @private
-   */
-  static _determineBidsIssueCode(hedIssue) {
-    if (hedIssue.internalCode === 'internalError') {
-      return 'HED_INTERNAL_ERROR'
-    }
-    if (hedIssue.level === 'warning') {
-      return 'HED_WARNING'
-    }
-    return 'HED_ERROR'
+    return groupBy(issues, (issue) => issue.severity)
   }
 
   /**

src/bids/types/tsv.js

@@ -42,7 +42,7 @@ export class BidsTsvFile extends BidsFile {
     if (typeof tsvData === 'string') {
       this.parsedTsv = parseTSV(tsvData)
     } else if (tsvData instanceof Map) {
-      this.parsedTsv = tsvData
+      this.parsedTsv = new Map(tsvData)
     } else if (isPlainObject(tsvData)) {
       this.parsedTsv = convertParsedTSVData(tsvData)
     } else {

src/bids/validator/tsvValidator.js

@@ -37,9 +37,9 @@ export class BidsHedTsvValidator extends BidsValidator {
     // Validate the BIDS bidsFile if it exists and return if there are errors
     if (this.bidsFile.mergedSidecar) {
       const issues = this.bidsFile.mergedSidecar.validate(this.hedSchemas)
-      const [errorIssues, warningIssues] = BidsHedIssue.splitErrors(issues)
-      this.errors.push(...errorIssues)
-      this.warnings.push(...warningIssues)
+      const splitErrors = BidsHedIssue.splitErrors(issues)
+      this.errors.push(...(splitErrors.error ?? []))
+      this.warnings.push(...(splitErrors.warning ?? []))
       if (this.errors.length > 0) {
         return
       }

src/schema/containers.js

@@ -1,5 +1,6 @@
+import lt from 'semver/functions/lt'
+
 import { IssueError } from '../issues/issues'
-import { getGenerationForSchemaVersion } from '../utils/hedData'
 
 /**
  * An imported HED 3 schema.
@@ -10,11 +11,6 @@ export class Schema {
    * @type {string}
    */
   version
-  /**
-   * The HED generation of this schema.
-   * @type {Number}
-   */
-  generation
   /**
    * The HED library schema name.
    * @type {string}
@@ -47,10 +43,10 @@ export class Schema {
     this.version = rootElement?.$?.version
     this.library = rootElement?.$?.library ?? ''
 
-    if (this.library) {
-      this.generation = 3
-    } else if (this.version) {
-      this.generation = getGenerationForSchemaVersion(this.version)
+    if (!this.library && this.version && lt(this.version, '8.0.0')) {
+      IssueError.generateAndThrow('deprecatedStandardSchemaVersion', {
+        version: this.version,
+      })
     }
 
     if (!this.library) {
@@ -93,7 +89,6 @@ export class PartneredSchema extends Schema {
     this.actualSchemas = actualSchemas
     this.withStandard = actualSchemas[0].withStandard
     this.library = undefined
-    this.generation = 3
   }
 }
 
@@ -186,38 +181,4 @@ export class Schemas {
       return null
     }
   }
-
-  /**
-   * The HED generation of this schema.
-   *
-   * If baseSchema is null, generation is set to 0.
-   * @type {Number}
-   */
-  get generation() {
-    if (this.schemas === null || this.schemas.size === 0) {
-      return 0
-    } else if (this.librarySchemas.size > 0) {
-      return 3
-    } else if (this.baseSchema) {
-      return this.baseSchema.generation
-    } else {
-      return 0
-    }
-  }
-
-  /**
-   * Whether this schema collection is for syntactic validation only.
-   * @returns {boolean}
-   */
-  get isSyntaxOnly() {
-    return this.generation === 0
-  }
-
-  /**
-   * Whether this schema collection comprises HED 3 schemas.
-   * @returns {boolean}
-   */
-  get isHed3() {
-    return this.generation === 3
-  }
 }

src/schema/schemaMerger.js

@@ -35,10 +35,6 @@ export default class PartneredSchemaMerger {
    * @private
    */
   _validate() {
-    if (!this.sourceSchemas.every((schema) => schema.generation === 3)) {
-      IssueError.generateAndThrowInternalError('Partnered schemas must be HED-3G schemas')
-    }
-
     for (const schema of this.sourceSchemas.slice(1)) {
       if (schema.withStandard !== this.destination.withStandard) {
         IssueError.generateAndThrow('differentWithStandard', {